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I have been getting a lot of questions regarding same sex marriage now that DOMA has been overturned, so I wanted to do a post on tax filing since things have now gotten...complex.
First things first, with DOMA out, you have to file your Federal return as if you were married if you were married in a state that legalized same-sex marriage at the time you were married, and you have not gotten a divorce. Marital status is determined as of 12/31 of the tax year. You can't just ignore it, even though it probably feels like that's what's been going on for several years. This means you have to file Married Filing Jointly, Married Filing Separately, or Head of Household (but only if you meet VERY SPECIFIC requirements regarding not living with your spouse and maintaining a home for children.) Single is right out.
Second, if you live in a state that recognizes same sex marriage (either by making them legal, or recognizing them for tax purposes (CO and MO)) you file the same way as you filed on the federal return (generally... some states let you go joint on one and separate on the other, but you just follow states rules.) Again, Single is right out.
What about the other states. Well, that's more complicated. Generally they require you to file Single or Head of Household, depending on your circumstances. Some require you to make a pro forma (this means fake) Federal return using the same status you use for state, in order to get the right numbers for the state. If you have different residency states, it only gets more complicated.
Rather than go over every situation, I'm going to try to provide a link to every state that doesn't fully recognize same-sex marriage so you can check what your state wants. I'm including Missouri and Colorado's regulations, since they allow you to match your Federal status, even though they don't recognize same-sex marriage.
These links are probably only good for 2013 taxes, and may even change for them, so double check when you file. (Montana deleted their link between the time I typed the state name, and the time I went to copy the address!)
UPDATE - Utah, it would seem, is allowing same sex couples to file jointly in 2013, though this is probably subject to change. Welcome to the UtahCoaster!
CALIFORNIA (different rules for Registered Domestic Partners)
Hope this helps! If it does, leave a TIP! Questions: firstname.lastname@example.org